Merge branch 'master' into gt/make-dd-work-for-non-raster

.github/workflows/black.yml

@@ -19,4 +19,5 @@ jobs:
       - uses: actions/setup-python@v2
       - uses: psf/black@stable
         with:
-          args: ". --check"
+          options: "--check --verbose --diff"
+          src: "setup.py landlab tests"

.github/workflows/changelog.yml

@@ -0,0 +1,26 @@
+name: Check
+
+on:
+  pull_request:
+    types: [labeled, unlabeled, opened, reopened, synchronize]
+
+jobs:
+  check-changelog-entry:
+    name: changelog entry
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          # `towncrier check` runs `git diff --name-only origin/main...`, which
+          # needs a non-shallow clone.
+          fetch-depth: 0
+
+      - name: Check changelog
+        if: "!contains(github.event.pull_request.labels.*.name, 'Skip Changelog')"
+        run: |
+          if ! pipx run towncrier check --compare-with origin/${{ github.base_ref }}; then
+          echo "Please see https://landlab.readthedocs.io/en/master/development/contribution/index.html?highlight=towncrier#news-entries for guidance."
+            false
+          fi
+

.github/workflows/docs.yml

@@ -1,22 +1,6 @@
 name: Documentation
 
-on:
-    push:
-        paths:
-            - "docs/**"
-            - "AUTHORS.rst"
-            - "CHANGES.rst"
-            - "CONTRIBUTING.rst"
-            - "LICENSE.rst"
-            - "README.rst"
-    pull_request:
-        paths:
-            - "docs/**"
-            - "AUTHORS.rst"
-            - "CHANGES.rst"
-            - "CONTRIBUTING.rst"
-            - "LICENSE.rst"
-            - "README.rst"
+on: [push, pull_request]
 
 jobs:
     build:
@@ -46,14 +30,9 @@ jobs:
           - name: Show conda installation info
             run: |
               conda info
-              conda list
     
           - name: Install dependencies
-            run: |
-              conda install mamba
-              mamba install --file=requirements.txt
-              pip install -r requirements-docs.txt
-              pip install -e .
+            run: pip install nox
 
           - name: Build documentation
-            run: make -C docs clean html
+            run: nox -s docs

.github/workflows/flake8.yml

@@ -23,5 +23,5 @@ jobs:
 
       - name: Lint
         run: |
-          pip install flake8
-          flake8 landlab tests
+          pip install nox
+          nox -s lint

.github/workflows/prerelease.yml

@@ -3,7 +3,7 @@ name: TestPyPI
 on:
   push:
     tags:
-      - v[0-9]+.[0-9]+.[0-9]+[ab][0-9]*
+      - 'v[0-9]+.[0-9]+.[0-9]+[ab][0-9]+'
 
 env:
   TWINE_USERNAME: __token__
@@ -20,22 +20,14 @@ jobs:
         shell: bash -l {0}
 
     strategy:
+      fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.7, 3.8, 3.9]
-        include:
-          - os: ubuntu-latest
-            platform: manylinux
-            python_versions: 'cp37-cp37m cp38-cp38 cp39-cp39'
-          - os: macos-latest
-            platform: macosx
-          - os: windows-latest
-            platform: win
-        exclude:
-          - os: ubuntu-latest
-            python-version: 3.7
-          - os: ubuntu-latest
-            python-version: 3.9
+    env:
+      CIBW_BUILD: 'cp38-* cp39-* cp310-*'
+      CIBW_SKIP: '*-musllinux_*'
+      CIBW_ARCHS_MACOS: "x86_64 arm64"
+      CIBW_ARCHS_LINUX: "auto aarch64"
 
     steps:
       - uses: actions/checkout@v2
@@ -47,33 +39,35 @@ jobs:
           channels: conda-forge
           channel-priority: true
 
+      - name: Set up QEMU
+        if: runner.os == 'Linux'
+        uses: docker/setup-qemu-action@v1
+        with:
+          platforms: all
+
+      - name: Install cibuildwheel
+        run: |
+          conda install pip
+          python --version
+          pip --version
+          python -m pip install cibuildwheel==2.3.0 twine
+
       - name: Show conda installation info
         run: |
           conda info
           conda list
 
-      - name: Install build environment
-        run: pip install twine wheel numpy cython
-
-      - name: Build macosx/win Python wheels
-        if: matrix.os == 'macos-latest' || matrix.os == 'windows-latest'
-        run: |
-          conda install mamba
-          mamba install --file=requirements.txt
-          python setup.py bdist_wheel
-
       - name: Build source distribution
         if: matrix.os == 'ubuntu-latest'
         run: |
-          python setup.py sdist
-          twine upload --skip-existing dist/*.tar.gz
+          pip install numpy
+          python setup.py sdist --dist-dir wheelhouse
+          twine upload --skip-existing wheelhouse/*.tar.gz
 
-      - name: Build manylinux Python wheels
-        if: matrix.os == 'ubuntu-latest'
-        uses: RalfG/python-wheels-manylinux-build@v0.3.3-manylinux2010_x86_64
-        with:
-          python-versions: ${{ matrix.python_versions }}
-          build-requirements: 'cython numpy'
+      - name: Build wheels
+        run: python -m cibuildwheel --output-dir wheelhouse
 
       - name: Upload distributions
-        run: twine upload --skip-existing dist/*-${{ matrix.platform }}*.whl
+        run: |
+          twine upload --skip-existing wheelhouse/*.whl
+

.github/workflows/release.yml

@@ -3,8 +3,8 @@ name: PyPI
 on:
   push:
     tags:
-      - v[0-9]+.[0-9]+.[0-9]+
-      - '!*[ab][0-9]*'
+      - 'v[0-9]+.[0-9]+.[0-9]+'
+      - '!v[0-9]+.[0-9]+.[0-9]+[ab][0-9]+'
 
 
 env:
@@ -21,22 +21,15 @@ jobs:
         shell: bash -l {0}
 
     strategy:
+      fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.7, 3.8, 3.9]
-        include:
-          - os: ubuntu-latest
-            platform: manylinux
-            python_versions: 'cp37-cp37m cp38-cp38 cp39-cp39'
-          - os: macos-latest
-            platform: macosx
-          - os: windows-latest
-            platform: win
-        exclude:
-          - os: ubuntu-latest
-            python-version: 3.7
-          - os: ubuntu-latest
-            python-version: 3.9
+
+    env:
+      CIBW_BUILD: 'cp38-* cp39-* cp310-*'
+      CIBW_SKIP: '*-musllinux_*'
+      CIBW_ARCHS_MACOS: "x86_64 arm64"
+      CIBW_ARCHS_LINUX: "auto aarch64"
 
     steps:
       - uses: actions/checkout@v2
@@ -48,33 +41,34 @@ jobs:
           channels: conda-forge
           channel-priority: true
 
+      - name: Set up QEMU
+        if: runner.os == 'Linux'
+        uses: docker/setup-qemu-action@v1
+        with:
+          platforms: all
+
+      - name: Install cibuildwheel
+        run: |
+          conda install pip
+          python --version
+          pip --version
+          python -m pip install cibuildwheel==2.3.0 twine
+
       - name: Show conda installation info
         run: |
           conda info
           conda list
 
-      - name: Install build environment
-        run: pip install twine wheel numpy cython
-
-      - name: Build macosx/win Python wheels
-        if: matrix.os == 'macos-latest' || matrix.os == 'windows-latest'
-        run: |
-          conda install mamba
-          mamba install --file=requirements.txt
-          python setup.py bdist_wheel
-
       - name: Build source distribution
         if: matrix.os == 'ubuntu-latest'
         run: |
-          python setup.py sdist
-          twine upload --skip-existing dist/*.tar.gz
+          pip install numpy
+          python setup.py sdist --dist-dir wheelhouse
+          twine upload --skip-existing wheelhouse/*.tar.gz
 
-      - name: Build manylinux Python wheels
-        if: matrix.os == 'ubuntu-latest'
-        uses: RalfG/python-wheels-manylinux-build@v0.3.3-manylinux2010_x86_64
-        with:
-          python-versions: ${{ matrix.python_versions }}
-          build-requirements: 'cython numpy'
+      - name: Build wheels
+        run: python -m cibuildwheel --output-dir wheelhouse
 
       - name: Upload distributions
-        run: twine upload --skip-existing dist/*-${{ matrix.platform }}*.whl
+        run: |
+          twine upload --skip-existing wheelhouse/*.whl

.github/workflows/test-notebooks.yml

@@ -2,6 +2,16 @@ name: Notebooks
 
 on: [push, pull_request]
 
+# on:
+#   push:
+#       paths:
+#           - "landlab/**"
+#           - "notebooks/**"
+#   pull_request:
+#       paths:
+#           - "landlab/**"
+#           - "notebooks/**"
+
 jobs:
   build-and-test:
     name: Check notebooks
@@ -21,7 +31,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ["3.9"]
 
     steps:
       - uses: actions/checkout@v2
@@ -35,24 +45,35 @@ jobs:
 
       - name: Show conda installation info
         run: |
+          conda install mamba
           conda info
           conda list
 
-      - name: Install requirements
+      - name: Install richdem requirements
         run: |
-          conda install mamba
-          mamba install --file=requirements.txt
+          mamba install richdem -c conda-forge
+          mamba list
+
+      - name: Install testing requirements
+        run: |
+          mamba install click pytest pytest-xdist pyyaml -c conda-forge
+          mamba list
+
+      - name: Install notebook requirements
+        run: |
+          mamba install --file=requirements-notebooks.txt -c conda-forge
           mamba list
 
       - name: Build and install package
         run: |
           pip install -e .
 
-      - name: Install testing dependencies
-        run: mamba install --file=requirements-testing.txt -c conda-forge
+      - name: Test jupyter notebooks are clean
+        run: python notebooks/run_notebook_checks.py notebooks
 
       - name: Test jupyter notebooks
+        env:
+          OPENTOPOGRAPHY_API_KEY: ${{ secrets.OPENTOPOGRAPHY_API_KEY }}
         run: |
           python -c 'import landlab; print(landlab.__version__)'
-          pip install -r requirements-notebooks.txt
-          pytest notebooks --run-notebook -vvv
+          pytest notebooks --run-notebook -n auto -vvv

.github/workflows/test.yml

@@ -2,6 +2,16 @@ name: Test
 
 on: [push, pull_request]
 
+# on:
+#   push:
+#       paths:
+#           - "landlab/**"
+#           - "tests/**"
+#   pull_request:
+#       paths:
+#           - "landlab/**"
+#           - "tests/**"
+
 jobs:
   build-and-test:
     name: Run the tests
@@ -21,7 +31,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ["3.8", "3.9", "3.10"]
 
     steps:
       - uses: actions/checkout@v2
@@ -38,23 +48,25 @@ jobs:
           conda info
           conda list
 
-      - name: Install requirements
+      - name: Install and test richdem engine
         run: |
           conda install mamba
-          mamba install --file=requirements.txt
-          mamba list
+          mamba install richdem -c conda-forge
+          python -c 'import _richdem'
 
       - name: Build and install package
         run: |
           pip install -e .
 
-      - name: Install testing dependencies
-        run: mamba install --file=requirements-testing.txt
+      - name: Install testing requirements
+        run: pip install -e .[testing]
 
       - name: Test
+        env:
+          HYPOTHESIS_PROFILE: "ci"
         run: |
           python -c 'import landlab; print(landlab.__version__)'
-          pytest --cov=landlab --cov-report=xml:$(pwd)/coverage.xml -vvv
+          pytest --cov=landlab --cov-report=xml:$(pwd)/coverage.xml -vvv -n auto
 
       - name: Coveralls
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.9'